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Gu L, Yuan W, Yang Y, Shen Y, An C, Xi W. In Situ TEM Tracking of Disconnection Motion and Atomic Cooperative Reorientation in the Oriented Attachment of Pt Nanoparticles. Nano Lett 2024. [PMID: 38661108 DOI: 10.1021/acs.nanolett.4c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The oriented attachment (OA) of nanoparticles (NPs) is an important crystal growth mechanism in many materials. However, a comprehensive understanding of the atomic-scale alignment and attachment processes is still lacking. We conducted in situ atomic resolution studies using high-resolution transmission electron microscopy to reveal how two Pt NPs coalesce into a single particle via OA, which involves the formation of atomic-scale links and a grain boundary (GB) between the NPs, as well as GB migration. Density functional theory calculations showed that the system energy changes as a function of the number of disconnections during the coalescence process. Additionally, the formation and annihilation processes of disconnection are always accompanied by the cooperative reorientation motion of atoms. These results further elucidate the growth mechanism of OA at the atomic scale, providing microscopic insights into OA dynamics and a framework for the development of processing strategies for nanocrystalline materials.
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Affiliation(s)
- Lin Gu
- School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Wenjuan Yuan
- Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Yufeng Yang
- Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Yongli Shen
- Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Changhua An
- School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Wei Xi
- School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
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2
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Poikela N, Laetsch DR, Hoikkala V, Lohse K, Kankare M. Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana. Genome Biol Evol 2024; 16:evae024. [PMID: 38482698 PMCID: PMC10972691 DOI: 10.1093/gbe/evae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 04/01/2024] Open
Abstract
Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.
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Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ville Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
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Sari I, Alrasheedi N, Ahmadein M, Djuansjah J, Hachani L, Zaidat K, Wu M, Kharicha A. Modeling Dendrite Coarsening and Remelting during Directional Solidification of Al-06wt.%Cu Alloy. Materials (Basel) 2024; 17:912. [PMID: 38399163 PMCID: PMC10890449 DOI: 10.3390/ma17040912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Research efforts have been dedicated to predicting microstructural evolution during solidification processes. The main secondary arm spacing controls the mushy zone's permeability. The aim of the current work was to build a simple sub-grid model that describes the growth and coarsening of secondary side dendrite arms. The idea was to reduce the complexity of the curvature distribution with only two adjacent side arms in concurrence. The model was built and applied to the directional solidification of Al-06wt%Cu alloy in a Bridgman experiment. The model showed its effectiveness in predicting coarsening phenomena during the solidification of Al-06wt%Cu alloy. The results showed a rapid growth of both arms at an earlier stage of solidification, followed by the remelting of the smaller arm. In addition, the results are in good agreement with an available time-dependent expression which covers the growth and coarsening. Such model can be implemented as a sub-grid model in volume average models for the prediction of the evolution of the main secondary arms spacing during macroscopic solidification processes.
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Affiliation(s)
- Ibrahim Sari
- Metallurgy Department, Montanuniversitaet of Leoben, Franz-Josef-Str. 18, 8700 Leoben, Austria (M.W.)
| | - Nashmi Alrasheedi
- Department of Mechanical Engineering, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia (J.D.)
| | - Mahmoud Ahmadein
- Department of Production Engineering and Mechanical Design, Tanta University, Tanta 31512, Egypt;
| | - Joy Djuansjah
- Department of Mechanical Engineering, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia (J.D.)
| | - Lakhdar Hachani
- Laboratoire Physique des Matériaux, Université Amar Telidji-Laghouat, Route de Ghardaia, BP 37G, Laghouat 03000, Algeria
| | - Kader Zaidat
- University Grenoble Alpes, Grenoble-INP, CNRS, SIMaP, 38400 Saint-Martin-d’Hères, France
| | - Menghuai Wu
- Metallurgy Department, Montanuniversitaet of Leoben, Franz-Josef-Str. 18, 8700 Leoben, Austria (M.W.)
| | - Abdellah Kharicha
- Metallurgy Department, Montanuniversitaet of Leoben, Franz-Josef-Str. 18, 8700 Leoben, Austria (M.W.)
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4
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Reta Dominguez CV, Wagner JR, Porfiri MC. Nanofibers from soybean hull insoluble polysaccharides as Pickering stabilizers in oil-in-water emulsions formulated under acidic conditions. J Sci Food Agric 2024; 104:125-133. [PMID: 37535855 DOI: 10.1002/jsfa.12897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Pickering emulsions are a kind of emulsion stabilized by solid particles. These particles generate a physical or mechanical barrier that provides long-term stability to emulsion. Cellulose nanofibers are effective Pickering emulsifiers given their long length, high flexibility and entanglement capability. In this work, soybean hull insoluble polysaccharides (HIPS) were used as source of cellulose nanofibers by using a combination of chemical and mechanical treatment. The chemical composition, morphology, flow behavior, water holding capacity (WHC) and emulsifying properties of the nanofibers were studied. RESULTS Nanofibers with diameters between 35 and 110 nm were obtained. The WHC increased significantly after the mechanical treatment, and the rheological behavior of the nanofibers was typical of cellulosic materials. Nanofibers were effective emulsifiers in oil-in-water (O/W) emulsions formulated under acidic conditions, without the need of using any additional surfactant. Emulsions were not affected by changes in the pH of the medium (3.00-5.00), and were stable to coalescence. CONCLUSION It is possible that cellulose nanofibers form an entangled network which acts as a mechanical steric barrier, providing stability to coalescence. These results are important for the development of effective O/W Pickering emulsifiers/stabilizers, with large applications in the food industry. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Camila V Reta Dominguez
- Laboratorio de Investigación en Funcionalidad y Tecnología de Alimentos (LIFTA), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352 (B1876BXD), Buenos Aires, Argentina
| | - Jorge R Wagner
- Laboratorio de Investigación en Funcionalidad y Tecnología de Alimentos (LIFTA), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352 (B1876BXD), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María C Porfiri
- Laboratorio de Investigación en Funcionalidad y Tecnología de Alimentos (LIFTA), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352 (B1876BXD), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Haque MR, Kubatko L. A global test of hybrid ancestry from genome-scale data. Stat Appl Genet Mol Biol 2024; 23:sagmb-2022-0061. [PMID: 38366619 DOI: 10.1515/sagmb-2022-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/27/2024] [Indexed: 02/18/2024]
Abstract
Methods based on the multi-species coalescent have been widely used in phylogenetic tree estimation using genome-scale DNA sequence data to understand the underlying evolutionary relationship between the sampled species. Evolutionary processes such as hybridization, which creates new species through interbreeding between two different species, necessitate inferring a species network instead of a species tree. A species tree is strictly bifurcating and thus fails to incorporate hybridization events which require an internal node of degree three. Hence, it is crucial to decide whether a tree or network analysis should be performed given a DNA sequence data set, a decision that is based on the presence of hybrid species in the sampled species. Although many methods have been proposed for hybridization detection, it is rare to find a technique that does so globally while considering a data generation mechanism that allows both hybridization and incomplete lineage sorting. In this paper, we consider hybridization and coalescence in a unified framework and propose a new test that can detect whether there are any hybrid species in a set of species of arbitrary size. Based on this global test of hybridization, one can decide whether a tree or network analysis is appropriate for a given data set.
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Affiliation(s)
- Md Rejuan Haque
- Division of Biostatistics, College of Public Health, and Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Laura Kubatko
- Department of Statistics and Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
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Xu S, Zhang T, Zhang X, Gui Q, Sun F, Zhang Y. Dynamics of the sedimentary bacterial communities in a plain river network: similar coalescence patterns with bacterioplankton communities driven by distinct assembly processes. Appl Environ Microbiol 2023; 89:e0146523. [PMID: 38092675 PMCID: PMC10734549 DOI: 10.1128/aem.01465-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/12/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Microorganisms play important roles in driving the biogeochemical cycles within river ecosystems. It has been suggested that hydrologic conditions could influence microbial communities in rivers, but their specific effects on the behaviours of microbial coalescence have not been thoroughly investigated. In this study, the dynamics of sedimentary bacterial communities within a plain river network were analyzed by amplicon sequencing followed by several ecological models to uncover the underlying assembly processes. Additionally, a comparative analysis between bacterioplankton communities and sedimentary bacterial communities was performed to unveil their coalescence patterns. The results suggested that similar coalescence patterns between sedimentary bacterial and bacterioplankton communities were driven by distinct assembly processes under dynamic hydrological conditions. These findings enhanced our understanding of microbial diversity features within river ecosystems.
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Affiliation(s)
- Sai Xu
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Tao Zhang
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Xinyi Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Qiyao Gui
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Fengbin Sun
- State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Yimin Zhang
- Ministry of Ecology and Environment, Nanjing Institute of Environmental Sciences, Nanjing, China
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7
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Shen Y, Su S, Xu T, Yin K, Yang K, Sun L. In Situ Transmission Electron Microscopy Investigation on Oriented Attachment of Nanodiamonds. Nano Lett 2023; 23:9602-9608. [PMID: 37812081 DOI: 10.1021/acs.nanolett.3c03300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Oriented attachment (OA) plays an important role in the assembly of nanoparticles and the regulation of their size and morphology, which is expected to be an effective means to modulate the properties of nanodiamonds (NDs). However, there remains a dearth of comprehensive investigation into the OA mechanism of NDs. Using in situ transmission electron microscopy, we conducted atomic-resolution investigation on the OA events of ND pairs under electron beam irradiation. The occurrence of an OA event is contingent upon the alignment between two ND surfaces, and the coalesced particles undergo recrystallization to form spherical shapes. Both experimental observations and molecular dynamics (MD) simulations reveal that ND pairs exhibit a preference for coalescing along the {111} surfaces. Additionally, MD simulations indicate that kinetic factors, such as contact surface area and contact angle, also influence the coalescence process.
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Affiliation(s)
- Yuting Shen
- School of Electronic and Information Engineering, Changshu Institute of Technology, Changshu 215500, P. R. China
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Collaborative Innovation Center for Micro/Nano Fabrication, Device and System, Southeast University, Nanjing 210096, P. R. China
| | - Shi Su
- School of Aeronautic Engineering, Nanjing Vocational University of Industry Technology, Nanjing 210023, P. R. China
| | - Tao Xu
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Collaborative Innovation Center for Micro/Nano Fabrication, Device and System, Southeast University, Nanjing 210096, P. R. China
| | - Kuibo Yin
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Collaborative Innovation Center for Micro/Nano Fabrication, Device and System, Southeast University, Nanjing 210096, P. R. China
| | - Kaishuai Yang
- School of Electronic and Information Engineering, Changshu Institute of Technology, Changshu 215500, P. R. China
| | - Litao Sun
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Collaborative Innovation Center for Micro/Nano Fabrication, Device and System, Southeast University, Nanjing 210096, P. R. China
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Chaturvedi J, Munthasir ATM, Nayak AK, Tripathi LN, Thilagar P, Jagirdar BR. Shape and Phase-Controlled One-Pot Synthesis of Air Stable Cationic AgCdS Nanocrystals, Optoelectronic and Electrochemical Hydrogen Evolution Studies. Small Methods 2023:e2300907. [PMID: 37849238 DOI: 10.1002/smtd.202300907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/24/2023] [Indexed: 10/19/2023]
Abstract
CdS-based materials are extensively studied for photocatalytic water splitting. By incorporating Ag+ into CdS nanomaterials, the catalyst's charge carrier dynamic can be tuned for photo-electrochemical devices. However, photo-corrosion and air-stability of the heterostructures limit the photocatalytic device's performance. Here, a one-pot, single molecular source synthesis of the air-stable AgCdS ternary semiconductor alloy nanostructures by heat-up method is reported. Monoclinic and hexagonal phases of the alloy are tuned by judicious choice of dodecane thiol (DDT), octadecyl amine (ODA), and oleyl amine (OLA) as capping agents. Transmission electron microscope (TEM) and powder X-ray diffraction characterization of the AgCdS alloy confirm the monoclinic and hexagonal phase (wurtzite) formation. The high-resolution TEM studies confirm the formation of AgCdS@DDT alloy nanorods and their shape transformation into nano-triangles. The nanoparticle coalescence is observed for ODA-capped alloys in the wurtzite phase. Moreover, OLA directs mixed crystal phases and anisotropic growth of alloy. Optical processes in AgCdS@DDT nano-triangles show mono-exponential decay (3.97 ± 0.01 ns). The monoclinic phase of the AgCdS@DDT nanorods exhibits higher electrochemical hydrogen evolution activity in neutral media as compared to the AgCdS@ODA/OLA alloy nanocrystals. DDT and OLA-capped alloys display current densities of 14.1 and 14.7 mA cm-2 , respectively, at 0.8 V (vs RHE).
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Affiliation(s)
- Jyotsna Chaturvedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Arpan Kumar Nayak
- Department of Physics, School of Advance Sciences, Vellore Institute of Technology, Vellore, 632014, India
| | - Laxmi Narayan Tripathi
- Department of Physics, School of Advance Sciences, Vellore Institute of Technology, Vellore, 632014, India
| | - Pakkirisamy Thilagar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Balaji R Jagirdar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
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Dubrovskii VG. Can Nanowires Coalesce? Nanomaterials (Basel) 2023; 13:2768. [PMID: 37887919 PMCID: PMC10609440 DOI: 10.3390/nano13202768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Coalescence of nanowires and other three-dimensional structures into continuous film is desirable for growing low-dislocation-density III-nitride and III-V materials on lattice-mismatched substrates; this is also interesting from a fundamental viewpoint. Here, we develop a growth model for vertical nanowires which, under rather general assumptions on the solid-like coalescence process within the Kolmogorov crystallization theory, results in a morphological diagram for the asymptotic coverage of a substrate surface. The coverage is presented as a function of two variables: the material collection efficiency on the top nanowire facet a and the normalized surface diffusion flux of adatoms from the NW sidewalls b. The full coalescence of nanowires is possible only when a=1, regardless of b. At a>1, which often holds for vapor-liquid-solid growth with a catalyst droplet, nanowires can only partly merge but never coalesce into continuous film. In vapor phase epitaxy techniques, the NWs can partly merge but never fully coalesce, while in the directional molecular beam epitaxy the NWs can fully coalesce for small enough contact angles of their droplets corresponding to a=1. The growth kinetics of nanowires and evolution of the coverage in the pre-coalescence stage is also considered. These results can be used for predicting and controlling the degree of surface coverage by nanowires and three-dimensional islands by tuning the surface density, droplet size, adatoms diffusivity, and geometry of the initial structures in the vapor-liquid-solid, selective area, or self-induced growth by different epitaxy techniques.
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Affiliation(s)
- Vladimir G Dubrovskii
- Faculty of Physics, St. Petersburg State University, Universitetskaya Emb. 13B, 199034 St. Petersburg, Russia
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10
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Fazekas ÁF, Gyulavári T, Pap Z, Bodor A, Laczi K, Perei K, Illés E, László Z, Veréb G. Effects of Different TiO 2/CNT Coatings of PVDF Membranes on the Filtration of Oil-Contaminated Wastewaters. Membranes (Basel) 2023; 13:812. [PMID: 37887984 PMCID: PMC10608089 DOI: 10.3390/membranes13100812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
Six different TiO2/CNT nanocomposite-coated polyvinylidene-fluoride (PVDF) microfilter membranes (including -OH or/and -COOH functionalized CNTs) were evaluated in terms of their performance in filtering oil-in-water emulsions. In the early stages of filtration, until reaching a volume reduction ratio (VRR) of ~1.5, the membranes coated with functionalized CNT-containing composites provided significantly higher fluxes than the non-functionalized ones, proving the beneficial effect of the surface modifications of the CNTs. Additionally, until the end of the filtration experiments (VRR = 5), notable flux enhancements were achieved with both TiO2 (~50%) and TiO2/CNT-coated membranes (up to ~300%), compared to the uncoated membrane. The irreversible filtration resistances of the membranes indicated that both the hydrophilicity and surface charge (zeta potential) played a crucial role in membrane fouling. However, a sharp and significant flux decrease (~90% flux reduction ratio) was observed for all membranes until reaching a VRR of 1.1-1.8, which could be attributed to the chemical composition of the oil. Gas chromatography measurements revealed a lack of hydrocarbon derivatives with polar molecular fractions (which can act as natural emulsifiers), resulting in significant coalescent ability (and less stable emulsion). Therefore, this led to a more compact cake layer formation on the surface of the membranes (compared to a previous study). It was also demonstrated that all membranes had excellent purification efficiency (97-99.8%) regarding the turbidity, but the effectiveness of the chemical oxygen demand reduction was slightly lower, ranging from 93.7% to 98%.
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Affiliation(s)
- Ákos Ferenc Fazekas
- Department of Biosystem Engineering, Faculty of Engineering, University of Szeged, Moszkvai Blvd. 9., H-6725 Szeged, Hungary
- Doctoral School of Environmental Sciences, University of Szeged, Rerrich Béla Sq. 1, H-6720 Szeged, Hungary
| | - Tamás Gyulavári
- Department of Applied and Environmental Chemistry, Institute of Chemistry, University of Szeged, Rerrich Béla Sq. 1, H-6720 Szeged, Hungary
| | - Zsolt Pap
- Department of Applied and Environmental Chemistry, Institute of Chemistry, University of Szeged, Rerrich Béla Sq. 1, H-6720 Szeged, Hungary
- Centre of Nanostructured Materials and Bio-Nano Interfaces, Institute for Interdisciplinary, Research on Bio-Nano-Sciences, Treboniu Laurian 42, RO-400271 Cluj-Napoca, Romania
- STAR-UBB Institute, Mihail Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
| | - Attila Bodor
- Department of Biotechnology, Institute of Biology, University of Szeged, Közép Alley 52, H-6726 Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, Hungarian Research Network, Temesvári Blvd. 62, H-6726 Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, Institute of Biology, University of Szeged, Közép Alley 52, H-6726 Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, Institute of Biology, University of Szeged, Közép Alley 52, H-6726 Szeged, Hungary
| | - Erzsébet Illés
- Department of Food Engineering, Faculty of Engineering, University of Szeged, Mars Sq. 7, H-6724 Szeged, Hungary
| | - Zsuzsanna László
- Department of Biosystem Engineering, Faculty of Engineering, University of Szeged, Moszkvai Blvd. 9., H-6725 Szeged, Hungary
| | - Gábor Veréb
- Department of Biosystem Engineering, Faculty of Engineering, University of Szeged, Moszkvai Blvd. 9., H-6725 Szeged, Hungary
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11
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Aidonidou E, Kalathaki I, Karageorgiou V, Ritzoulis C. Capturing the onset of oral processing: Merging of a model food emulsion drop with saliva. J Texture Stud 2023; 54:595-598. [PMID: 37134026 DOI: 10.1111/jtxs.12752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/26/2022] [Accepted: 03/13/2023] [Indexed: 05/04/2023]
Abstract
The events occurring before and during the merging of a model liquid food emulsion with saliva have been captured ex vivo using confocal microscopy. In the order of a few seconds, millimeter-sized drops of liquid food and saliva touch and are deformed; the two surfaces eventually collapse, resulting in the merging of the two phases, in a process reminiscent of emulsion droplets coalescing. The model droplets then surge into saliva. Based on this, two distinct stages can be distinguished for the insertion of a liquid food into the oral cavity: A first phase where two intact phases co-exist, and the individual viscosities and saliva-liquid food tribology should be important to texture perception; and a second stage, dominated by the rheological properties of the liquid food-saliva mixture. The importance of the surface properties of saliva and liquid food are highlighted, as they may influence the merging of the two phases.
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Affiliation(s)
- Eleni Aidonidou
- Department of Food Science and Technology, International Hellenic University, Thessaloniki, Greece
| | - Iasmi Kalathaki
- Department of Food Science and Technology, International Hellenic University, Thessaloniki, Greece
| | - Vassilis Karageorgiou
- Department of Food Science and Technology, International Hellenic University, Thessaloniki, Greece
| | - Christos Ritzoulis
- Department of Food Science and Technology, International Hellenic University, Thessaloniki, Greece
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
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12
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Wciślik W, Lipiec S. Voids Development in Metals: Numerical Modelling. Materials (Basel) 2023; 16:4998. [PMID: 37512271 PMCID: PMC10384217 DOI: 10.3390/ma16144998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
The article is a continuation of two previous review papers on the fracture mechanism of structural metals through the nucleation, growth and coalescence of voids. In the present paper, the literature on the numerical modelling of void nucleation and development has been reviewed. The scope of the work does not include porous material models and their numerical implementation. As part of the discussion on void initiation, nucleation around second phase particles and nucleation as an effect of the discontinuity of the crystal structure were discussed separately. The basic void cell models, finite element method (FEM) models of periodically distributed particles/voids and models based on the results of the observations of the actual microstructure of materials have been characterised. Basic issues related to the application of the cohesive approach in void nucleation modelling have been considered. A separate issue is the characteristics of atomistic simulations and peridynamic modelling, which have been developed in recent years. Numerical approaches to modelling the growth and coalescence of voids are described, with particular emphasis on the influence of the stress state and strain localisation. Basic conclusions from the simulation are presented, pointing to the contribution of FEM modelling to the understanding of microstructural phenomena leading to ductile fracture.
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Affiliation(s)
- Wiktor Wciślik
- Faculty of Civil Engineering and Architecture, Kielce University of Technology, 25-314 Kielce, Poland
| | - Sebastian Lipiec
- Faculty of Mechatronics and Mechanical Engineering, Kielce University of Technology, 25-314 Kielce, Poland
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13
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Wehbe M, Charles M, Baril K, Alloing B, Pino Munoz D, Labchir N, Zuniga-Perez J, Detlefs C, Yildirim C, Gergaud P. Study of GaN coalescence by dark-field X-ray microscopy at the nanoscale. J Appl Crystallogr 2023; 56:643-649. [PMID: 37284275 PMCID: PMC10241046 DOI: 10.1107/s160057672300287x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/26/2023] [Indexed: 06/08/2023] Open
Abstract
This work illustrates the potential of dark-field X-ray microscopy (DFXM), a 3D imaging technique of nanostructures, in characterizing novel epitaxial structures of gallium nitride (GaN) on top of GaN/AlN/Si/SiO2 nano-pillars for optoelectronic applications. The nano-pillars are intended to allow independent GaN nanostructures to coalesce into a highly oriented film due to the SiO2 layer becoming soft at the GaN growth temperature. DFXM is demonstrated on different types of samples at the nanoscale and the results show that extremely well oriented lines of GaN (standard deviation of 0.04°) as well as highly oriented material for zones up to 10 × 10 µm2 in area are achieved with this growth approach. At a macroscale, high-intensity X-ray diffraction is used to show that the coalescence of GaN pyramids causes misorientation of the silicon in the nano-pillars, implying that the growth occurs as intended (i.e. that pillars rotate during coalescence). These two diffraction methods demonstrate the great promise of this growth approach for micro-displays and micro-LEDs, which require small islands of high-quality GaN material, and offer a new way to enrich the fundamental understanding of optoelectronically relevant materials at the highest spatial resolution.
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Affiliation(s)
- Maya Wehbe
- Univ. Grenoble Alpes, CEA-LETI, 38000 Grenoble, France
- MINES Paris, PSL Research University, CEMEF – Center for Material Forming, CNRS UMR 7635, BP 207, 1 rue Claude Daunesse, 06904 Sophia Antipolis Cedex, France
| | | | - Kilian Baril
- Univ. Côte d’Azur, CNRS, CRHEA, Rue Bernard Gregory, 06560 Valbonne, France
| | - Blandine Alloing
- Univ. Côte d’Azur, CNRS, CRHEA, Rue Bernard Gregory, 06560 Valbonne, France
| | - Daniel Pino Munoz
- MINES Paris, PSL Research University, CEMEF – Center for Material Forming, CNRS UMR 7635, BP 207, 1 rue Claude Daunesse, 06904 Sophia Antipolis Cedex, France
| | - Nabil Labchir
- Univ. Grenoble Alpes, CNRS, CEA/LETI-Minatec, Grenoble INP, LTM, F-38054 Grenoble, France
| | - Jesús Zuniga-Perez
- Univ. Côte d’Azur, CNRS, CRHEA, Rue Bernard Gregory, 06560 Valbonne, France
- MajuLab, International Research Laboratory IRL 3654, CNRS, Université Côte d’Azûr, Sorbonne Université, National University of Singapore, Nanyang Technological University, Singapore, Singapore
| | - Carsten Detlefs
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France
| | - Can Yildirim
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France
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14
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Ngo QP, Yuan W, Wu YCM, Swager TM. Emulsion Assembly of Graphene Oxide/Polymer Composite Membranes. ACS Appl Mater Interfaces 2023; 15:21384-21393. [PMID: 37071537 DOI: 10.1021/acsami.3c02636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Graphene oxide/polymer composite water filtration membranes were developed via coalescence of graphene oxide (GO) stabilized Pickering emulsions around a porosity-generating polymer. Triptycene poly(ether ether sulfone)-CH2NH2:HCl polymer interacts with the GO at the water-oil interface, resulting in stable Pickering emulsions. When they are deposited and dried on polytetrafluoroethylene substrate, the emulsions fuse to form a continuous GO/polymer composite membrane. X-ray diffraction and scanning electron microscopy demonstrate that the intersheet spacing and thickness of the membranes increased with increasing polymer concentration, confirming the polymer as the spacer between the GO sheets. The water filtration capability of the composite membranes was tested by removing Rose Bengal from water, mimicking separations of weak black liquor waste. The composite membrane achieved 65% rejection and 2500 g m-2 h-1 bar-1. With high polymer and GO loading, composite membranes give superior rejection and permeance performance when compared with a GO membrane. This methodology for fabrication membranes via GO/polymer Pickering emulsions produces membranes with a homogeneous morphology and robust chemical separation strength.
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Affiliation(s)
- Quynh P Ngo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Weize Yuan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - You-Chi Mason Wu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy M Swager
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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Murphy JG, Raybin JG, Ansay GE, Sibener SJ. Spatiotemporal Mapping of Hole Nucleation and Growth during Block Copolymer Terracing with High-Speed Atomic Force Microscopy. ACS Nano 2023; 17:5644-5652. [PMID: 36912602 DOI: 10.1021/acsnano.2c11672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
As a platform for investigating two-dimensional phase separation, we track the structural evolution of block copolymer thin films during thermal annealing with environmentally controlled atomic force microscopy (AFM). Upon thermal annealing, block copolymer films with incommensurate thickness separate into a terraced morphology decorated with holes. With in situ imaging at 200 °C, we follow the continuous progression of terrace formation in a single region of a cylinder-forming poly(styrene-block-methyl methacrylate) thin film, beginning with the disordered morphology on an unpatterned silicon substrate and continuing through nucleation and coarsening stages. Topographic AFM imaging with nanoscale resolution simultaneously captures ensemble hole growth statistics while locally tracking polymer diffusion through measurements of the film thickness. At early times, we observe homogeneous hole nucleation and isotropic growth, with kinetics following the predictions of classical nucleation theory. At later times, however, we find anomalous hole growth which arises due to the combination of Ostwald ripening and coalescence mechanisms. In each case, our real-space observations highlight the importance of hole interactions for determining coarsening kinetics, mediated either through the interconnected phase for Ostwald ripening or through binary collision events for coalescence.
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Affiliation(s)
- Julia G Murphy
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jonathan G Raybin
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Genevieve E Ansay
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Steven J Sibener
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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16
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Erratum: Convergent morphological evolution in Silene Sect. Italicae (Caryophyllaceae) in the Mediterranean Basin. Front Plant Sci 2023; 14:1182244. [PMID: 37021315 PMCID: PMC10067872 DOI: 10.3389/fpls.2023.1182244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.695958.].
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17
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Claesen J, Rockwood A, Gorshkov M, Valkenborg D. The isotope distribution: A rose with thorns. Mass Spectrom Rev 2023. [PMID: 36744702 DOI: 10.1002/mas.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 06/18/2023]
Abstract
The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.
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Affiliation(s)
- Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Alan Rockwood
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mikhail Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Dirk Valkenborg
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
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18
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Solano E, Dendooven J, Deduytsche D, Poonkottil N, Feng JY, Roeffaers MBJ, Detavernier C, Filez M. Metal Nanocatalyst Sintering Interrogated at Complementary Length Scales. Small 2023; 19:e2205217. [PMID: 36445117 DOI: 10.1002/smll.202205217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Metal nanoparticle (NP) sintering is a prime cause of catalyst degradation, limiting its economic lifetime and viability. To date, sintering phenomena are interrogated either at the bulk scale to probe averaged NP properties or at the level of individual NPs to visualize atomic motion. Yet, "mesoscale" strategies which bridge these worlds can chart NP populations at intermediate length scales but remain elusive due to characterization challenges. Here, a multi-pronged approach is developed to provide complementary information on Pt NP sintering covering multiple length scales. High-resolution scanning electron microscopy (HRSEM) and Monte Carlo simulation show that the size evolution of individual NPs depends on the number of coalescence events they undergo during their lifetime. In its turn, the probability of coalescence is strongly dependent on the NP's mesoscale environment, where local population heterogeneities generate NP-rich "hotspots" and NP-free zones during sintering. Surprisingly, advanced in situ synchrotron X-ray diffraction shows that not all NPs within the small NP sub-population are equally prone to sintering, depending on their crystallographic orientation on the support surface. The demonstrated approach shows that mesoscale heterogeneities in the NP population drive sintering and mitigation strategies demand their maximal elimination via advanced catalyst synthesis strategies.
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Affiliation(s)
- Eduardo Solano
- NCD-SWEET beamline, ALBA synchrotron light source, Cerdanyola del Vallès, 08290, Spain
| | - Jolien Dendooven
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
| | - Davy Deduytsche
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
| | - Nithin Poonkottil
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
| | - Ji-Yu Feng
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
| | - Maarten B J Roeffaers
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), KU Leuven, Celestijnenlaan, 200F, Leuven, 3001, Belgium
| | - Christophe Detavernier
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
| | - Matthias Filez
- Conformal Coating of Nanomaterials (CoCooN), Ghent University, Krijgslaan 281/S1, Ghent, 9000, Belgium
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), KU Leuven, Celestijnenlaan, 200F, Leuven, 3001, Belgium
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19
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Soltanahmadi S, Bryant M, Sarkar A. Insights into the Multiscale Lubrication Mechanism of Edible Phase Change Materials. ACS Appl Mater Interfaces 2023; 15:3699-3712. [PMID: 36633252 PMCID: PMC9880949 DOI: 10.1021/acsami.2c13017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Investigation of a lubrication behavior of phase change materials (PCM) can be challenging in applications involving relative motion, e.g., sport (ice skating), food (chocolates), energy (thermal storage), apparel (textiles with PCM), etc. In oral tribology, a phase change often occurs in a sequence of dynamic interactions between the ingested PCM and oral surfaces from a licking stage to a saliva-mixed stage at contact scales spanning micro- (cellular), meso- (papillae), and macroscales. Often the lubrication performance and correlations across length scales and different stages remain poorly understood due to the lack of testing setups mimicking real human tissues. Herein, we bring new insights into lubrication mechanisms of PCM using dark chocolate as an exemplar at a single-papilla (meso)-scale and a full-tongue (macro) scale covering the solid, molten, and saliva-mixed states, uniting highly sophisticated biomimetic oral surfaces with in situ tribomicroscopy for the first time. Unprecedented results from this study supported by transcending lubrication theories reveal how the tribological mechanism in licking shifted from solid fat-dominated lubrication (saliva-poor regime) to aqueous lubrication (saliva-dominant regime), the latter resulted in increasing the coefficient of friction by at least threefold. At the mesoscale, the governing mechanisms were bridging of cocoa butter in between confined cocoa particles and fat coalescence of emulsion droplets for the molten and saliva-mixed states, respectively. At the macroscale, a distinctive hydrodynamic viscous film formed at the interface governing the speed-dependent lubrication behavior indicates the striking importance of multiscale analyses. New tribological insights across different stages and scales of phase transition from this study will inspire rational design of the next generation of PCM and solid particle-containing materials.
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Affiliation(s)
- Siavash Soltanahmadi
- Food
Colloids and Bioprocessing Group, School of Food Science and Nutrition, University of Leeds, LeedsLS2 9JT, U.K.
| | - Michael Bryant
- Institute
of Functional Surfaces, School of Mechanical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
| | - Anwesha Sarkar
- Food
Colloids and Bioprocessing Group, School of Food Science and Nutrition, University of Leeds, LeedsLS2 9JT, U.K.
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20
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Watanabe K, Munakata H, Ueno K, Inoue H, Uyama M, Takahashi Y, Tsuchiya K, Sakai K, Sakai H. Novel O/W Emulsions by Utilizing a Vesicle/Disc Transformation of Polyether Modified Silicone. J Oleo Sci 2023; 72:693-708. [PMID: 37380485 DOI: 10.5650/jos.ess22392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Emulsification is an important technology in the field of cosmetics and household products. Emulsions are in non-equilibrium state; therefore, the products vary depending on the preparation process, and their state changes with time. Furthermore, it is known empirically that different types of oils have different emulsification properties (preparation and stability). For these reasons, the variables in emulsification research are numerous and complicated to analyze. As a result, many industrial applications have had to rely on empirical rules. In this study, emulsions with a lamellar liquid crystalline phase as an adsorption layer at the emulsion interface were investigated. The characteristics of O/W emulsions formed with the excess solvent phases (aqueous and oil phases) separated from the lamellar liquid crystalline phase were investigated based on the phase equilibrium of the ternary system.As a result, it was found that by agitating the aqueous phase containing dispersed vesicles of emulsifier (polyether modified silicone) together with the oil phase, an emulsion with a uniform interfacial membrane of lamellar liquid crystalline phase could be obtained. The emulsions prepared by this method were found to have good stability against coalescence. The process of transformation from vesicles to the uniform liquid crystal interfacial membrane during the emulsification process was clarified by a freeze-fracture transmission electron micrograph and the calculation of interfacial membrane thickness based on precise particle size analysis. Furthermore, the emulsification properties of polyether-modified silicones were clarified using polar oils and silicone oils, which are a combination of high/low and low/high compatibility with hydrophilic (polyethylene glycol) and lipophilic (polydimethylsiloxane) groups of polyether modified silicone, respectively. It is expected that this research will lead to the evolution of various functionalities in products in the fields of cosmetics, household products, food, pharmaceuticals, paint and others.
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Affiliation(s)
| | | | | | | | | | | | - Koji Tsuchiya
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science
| | - Kenichi Sakai
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science
| | - Hideki Sakai
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science
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21
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Liu S, Zhang H, Yuan S. Hydrophilic Silica Nanoparticles in O/W Emulsion: Insights from Molecular Dynamics Simulation. Molecules 2022; 27:molecules27238407. [PMID: 36500501 PMCID: PMC9740303 DOI: 10.3390/molecules27238407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
Previous studies have been carried out on the effect of silica nanoparticles (SNPs) on the stability of oil-water emulsions. However, the combining configuration of SNPs and oil droplets at the molecular level and the effect of SNP content on the coalescence behavior of oil droplets cannot be obtained through experiments. In this paper, molecular dynamics (MD) simulation was performed to investigate the adsorption configuration of hydrophilic SNPs in an O/W emulsion system, and the effect of adsorption of SNPs on coalescence of oil droplets. The simulation results showed: (i) SNPs adsorbed on the surface of oil droplets, and excessive SNPs self-aggregated and connected by hydrogen bonds. (ii) Partially hydrophilic asphaltene and resin molecules formed adsorption configurations with SNPs, which changed the distribution of oil droplet components. Furthermore, compared with hydrophobic asphaltene, the hydrophilic asphaltene was easier to combine with SNPs. (iii) SNPs would extend the oil droplet coalescence time, and the π-π stacking structures were formed between asphaltene and asphaltene or resin molecules to enhance the connection between oil droplets during the oil droplet contact process. (iv) Enough SNPs tightly wrapped around the oil droplet, similar to the formation of a rigid film on the surface of an oil droplet, which hindered the contact and coalescence of components between oil droplets.
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Affiliation(s)
- Shasha Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250100, China
| | - Hengming Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Shiling Yuan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
- Correspondence:
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22
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Szép E, Trubenová B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Mol Ecol Resour 2022; 22:2941-2955. [PMID: 35765749 PMCID: PMC9796524 DOI: 10.1111/1755-0998.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.
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Affiliation(s)
- Enikő Szép
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria
| | - Barbora Trubenová
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria,Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Katalin Csilléry
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
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23
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Yu J, Jin H, Wang Q, Wei X, Chen H, Wang Y. Coalescence of Au-Pd Nanoropes and their Application as Enhanced Electrocatalysts for the Oxygen Reduction Reaction. Small 2022; 18:e2203458. [PMID: 36123144 DOI: 10.1002/smll.202203458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Lattice distortions and defects can lead to a strain effect that greatly affects the electronic structure of the noble metal surface and the chemical adsorption of ligands on the surfaces. Introducing defects is an efficient strategy to improve the activity of noble metal catalysts. Herein, a fusion approach is developed to fine-tune the defects and lattice strain in Au-Pd nanowires. Specifically, braided strands in Au-Pd nanoropes gradually coalesce to form solid nanowires upon H2 O2 treatment and heating, leading to a series of Au-Pd nanowires with various amounts of defects. Owing to the 1D morphology, as well as the optimized lattice strain and surface electronic structure, the intermediate Au-Pd nanowire obtained after 60 min heating (denoted as Au-Pd NW60 ) exhibits excellent catalytic activity and stability toward the oxygen reduction reaction, with the half-wave potential at 0.918 V, 45 mV higher than that of the commercial Pt/C; and specific activity reaches up to 1.7 mA cm-2 , 7.3 times higher than that of the Pt/C.
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Affiliation(s)
- Jialong Yu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Hui Jin
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Qian Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Xiaoliang Wei
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Hongyu Chen
- School of Science, Westlake University, Hangzhou, 310064, P. R. China
| | - Yawen Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
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24
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Yue S, Yuan W, Deng Z, Xi W, Shen Y. In Situ TEM Observation of the Atomic Transport Process during the Coalescence of Au Nanoparticles. Nano Lett 2022; 22:8115-8121. [PMID: 36197114 DOI: 10.1021/acs.nanolett.2c02491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In practical applications, the coalescence of metal nanoparticles (NPs) is a major factor affecting their physical chemistry properties. Currently, due to a lack of understanding of the atomic-level mechanisms during the nucleation and growth stages of coalescence, the correlation between the different dynamic factors in the different stages of NP coalescence is unclear. In this study, we used advanced in situ characterization techniques to observe the formation of atomic material transport channels (Au chains) during the initiation of coalescence nucleation. We focused on the movement and migration states of Au atoms and discovered an atomic ordered arrangement growth mechanism that occurs after the completion of nucleation. Simultaneously, we used density functional theory to reveal the formation principle of Au chains. These findings improve our understanding of the atomic-scale coalescence process, which can provide a new perspective for further research on coalescence atomic dynamics.
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Affiliation(s)
- Shengnan Yue
- Center for Electron Microscopy and Tianjin Key Laboratory of Advanced Functional Porous Materials, Institute for New Energy Materials & Low-Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Wenjuan Yuan
- Center for Electron Microscopy and Tianjin Key Laboratory of Advanced Functional Porous Materials, Institute for New Energy Materials & Low-Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Ziliang Deng
- Center for Electron Microscopy and Tianjin Key Laboratory of Advanced Functional Porous Materials, Institute for New Energy Materials & Low-Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Wei Xi
- Center for Electron Microscopy and Tianjin Key Laboratory of Advanced Functional Porous Materials, Institute for New Energy Materials & Low-Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Yongli Shen
- Center for Electron Microscopy and Tianjin Key Laboratory of Advanced Functional Porous Materials, Institute for New Energy Materials & Low-Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
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25
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Wciślik W, Lipiec S. Void-Induced Ductile Fracture of Metals: Experimental Observations. Materials (Basel) 2022; 15:6473. [PMID: 36143784 PMCID: PMC9506433 DOI: 10.3390/ma15186473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The paper presents a literature review on the development of microvoids in metals, leading to ductile fracture associated with plastic deformation, without taking into account the cleavage mechanism. Particular emphasis was placed on the results of observations and experimental studies of the characteristics of the phenomenon itself, without in-depth analysis in the field of widely used FEM modelling. The mechanism of void development as a fracture mechanism is presented. Observations of the nucleation of voids in metals from the turn of the 1950s and 1960s to the present day were described. The nucleation mechanisms related to the defects of the crystal lattice as well as those resulting from the presence of second-phase particles were characterised. Observations of the growth and coalescence of voids were presented, along with the basic models of both phenomena. The modern research methods used to analyse changes in the microstructure of the material during plastic deformation are discussed. In summary, it was indicated that understanding the microstructural phenomena occurring in deformed material enables the engineering of the modelling of plastic fracture in metals.
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Affiliation(s)
- Wiktor Wciślik
- Faculty of Civil Engineering and Architecture, Kielce University of Technology, 25-314 Kielce, Poland
| | - Sebastian Lipiec
- Faculty of Mechatronics and Mechanical Engineering, Kielce University of Technology, 25-314 Kielce, Poland
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26
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Yan X, Ji B, Feng L, Wang X, Yang D, Rabbi KF, Peng Q, Hoque MJ, Jin P, Bello E, Sett S, Alleyne M, Cropek DM, Miljkovic N. Particulate-Droplet Coalescence and Self-Transport on Superhydrophobic Surfaces. ACS Nano 2022; 16:12910-12921. [PMID: 35960260 DOI: 10.1021/acsnano.2c05267] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Particulate transport from surfaces governs a variety of phenomena including fungal spore dispersal, bioaerosol transmission, and self-cleaning. Here, we report a previously unidentified mechanism governing passive particulate removal from superhydrophobic surfaces, where a particle coalescing with a water droplet (∼10 to ∼100 μm) spontaneously launches. Compared to previously discovered coalescence-induced binary droplet jumping, the reported mechanism represents a more general capillary-inertial dominated transport mode coupled with particle/droplet properties and is typically mediated by rotation in addition to translation. Through wetting and momentum analyses, we show that transport physics depends on particle/droplet density, size, and wettability. The observed mechanism presents a simple and passive pathway to achieve self-cleaning on both artificial as well as biological materials as confirmed here with experiments conducted on butterfly wings, cicada wings, and clover leaves. Our findings provide insights into particle-droplet interaction and spontaneous particulate transport, which may facilitate the development of functional surfaces for medical, optical, thermal, and energy applications.
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Affiliation(s)
- Xiao Yan
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Bingqiang Ji
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lezhou Feng
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xiong Wang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Daolong Yang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kazi Fazle Rabbi
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Qi Peng
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Muhammad Jahidul Hoque
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Puhang Jin
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Elizabeth Bello
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Soumyadip Sett
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marianne Alleyne
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Donald M Cropek
- Construction Engineering Research Laboratory, U.S. Army Engineer Research and Development Center, Champaign, Illinois 61822, United States
| | - Nenad Miljkovic
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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27
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Naciri Y, Toprak Z, Prentice HC, Hugot L, Troia A, Burgarella C, Gradaille JL, Jeanmonod D. Convergent Morphological Evolution in Silene Sect. Italicae (Caryophyllaceae) in the Mediterranean Basin. Front Plant Sci 2022; 13:695958. [PMID: 35903238 PMCID: PMC9319200 DOI: 10.3389/fpls.2022.695958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Recent divergence can obscure species boundaries among closely related taxa. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. The delimitation of other species (e.g., Silene nemoralis, S. nodulosa and S. andryalifolia) was more challenging. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. Species from the Western Mediterranean Basin showed more conflicting species boundaries than species from the Eastern Mediterranean Basin, where there are fewer but better-delimited species. Significant positive correlations were found between an estimation of the effective population size of the taxa and their extent of occurrence (EOO) or area of occupancy (AOO), and negative but non-significant correlations between the former and the posterior probability (PP) of the corresponding clades. These correlations might suggest a lower impact of incomplete lineage sorting in species with low effective population sizes and small distributional ranges compared with that in species inhabiting large areas. Finally, we confirmed that S. italica and S. nemoralis are distinct species, that S. nemoralis might furthermore include two different species and that S. velutina from Corsica and S. hicesiae from the Lipari Islands are sister species.
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Affiliation(s)
- Yamama Naciri
- Unité Systématique et Médiation, Conservatoire et Jardin botaniques de Genève, Geneva, Switzerland
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Zeynep Toprak
- Unité Systématique et Médiation, Conservatoire et Jardin botaniques de Genève, Geneva, Switzerland
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Department of Molecular Biology and Genetic, Faculty of Sciences, University of Dicle, Diyarbakir, Turkey
| | | | - Laetitia Hugot
- Conservatoire botanique national de Corse, Office de l’Environment de la Corse, Corte, France
| | - Angelo Troia
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | | | | | - Daniel Jeanmonod
- Unité Systématique et Médiation, Conservatoire et Jardin botaniques de Genève, Geneva, Switzerland
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
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28
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Abstract
Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.
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Affiliation(s)
- Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Dan Vanderpool
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana, USA
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29
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Cowell TW, Dobria A, Han HS. Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis. ACS Appl Mater Interfaces 2022; 14:20528-20537. [PMID: 35502700 DOI: 10.1021/acsami.1c22692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.
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Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Andrew Dobria
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave., Urbana, Illinois 61801, United States
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30
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Retout M, Mantri Y, Jin Z, Zhou J, Noël G, Donovan B, Yim W, Jokerst JV. Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers. ACS Nano 2022; 16:6165-6175. [PMID: 35377141 PMCID: PMC9530071 DOI: 10.1021/acsnano.1c11643] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report the peptide-programmed fractal assembly of silver nanoparticles (AgNPs) in a diffusion-limited aggregation (DLA) mode, and this change in morphology generates a significant color change. We show that peptides with specific repetitions of defined amino acids (i.e., arginine, histidine, or phenylalanine) can induce assembly and coalescence of the AgNPs (20 nm) into a hyperbranched structure (AgFSs) (∼2 μm). The dynamic process of this assembly was systematically investigated, and the extinction of the nanostructures can be modulated from 400 to 600 nm by varying the peptide sequences and molar ratio. According to this rationale, two strategies of SARS-CoV-2 detection were investigated. The activity of the main protease (Mpro) involved in SARS-CoV-2 was validated with a peptide substrate that can bridge the AgNPs after the proteolytic cleavage. A sub-nanomolar limit of detection (0.5 nM) and the capacity to distinguish by the naked eye in a wide concentration range (1.25-30 nM) were achieved. Next, a multichannel sensor-array based on multiplex peptides that can visually distinguish SARS-CoV-2 proteases from influenza proteases in doped human samples was investigated.
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Affiliation(s)
| | | | | | | | - Grégoire Noël
- Functional and Evolutionary Entomology-Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
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31
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Abstract
Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.
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Affiliation(s)
- Gordon F Custer
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Luana Bresciani
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
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32
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Tian Y, Shi P, Xu L, Qiu S, Zhu R. Numerical Modeling of Transient Two-Phase Flow and the Coalescence and Breakup of Bubbles in a Continuous Casting Mold. Materials (Basel) 2022; 15:2810. [PMID: 35454503 DOI: 10.3390/ma15082810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
Abstract
The multiphase flow and spatial distribution of bubbles inside a continuous casting (CC) mold is a popular research issue due to its direct impact on the quality of the CC slab. The behavior of bubbles in the mold, and how they coalesce and break apart, have an important influence on the flow pattern and entrapment of bubbles. However, due to the limitations of experiments and measurement methods, it is impossible to directly observe the multiphase flow and bubble distribution during the CC process. Thus, a three-dimensional mathematical model which combined the large eddy simulation (LES) turbulent model, VOF multiphase model, and discrete phase model (DPM) was developed to study the transient two-phase flow and spatial distribution of bubbles in a continuous casting mold. The interaction between the liquid and bubbles and the coalescence, bounce, and breakup of bubbles were considered. The measured meniscus speed and bubble diameter were in good agreement with the measured results. The meniscus speed increased first and then decreased from the nozzle to the narrow face, with a maximum value of 0.07 m/s, and appeared at 1/4 the width of the mold. The current mathematical model successfully predicted the transient asymmetric two-phase flow and completely reproduced the coalescence, bounce, and breakup of bubbles in the mold. The breakup mainly occurred near the bottom of the submerged entry nozzle (SEN) due to the strong turbulent motion of the molten steel after hitting the bottom of the SEN. The average bubble diameter was about 0.6 mm near the nozzle and gradually decreased to 0.05 mm from the nozzle to the narrow face. The larger bubbles floated up near the SEN due to the effect of their greater buoyancy, while the small bubbles were distributed discretely in the entire mold with the action of the molten steel jet. Overall, the bubbles were distributed in a fan shape. The largest concentration of bubbles was in the lower part of the SEN and the upper edge of the SEN outlet.
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33
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Lee SE, Yoon IS, Hwang YS. Abscisic acid activation of oleosin gene HvOle3 expression prevents the coalescence of protein storage vacuoles in barley aleurone cells. J Exp Bot 2022; 73:817-834. [PMID: 34698829 DOI: 10.1093/jxb/erab471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Protein storage vacuoles (PSVs) in aleurone cells coalesce during germination, and this process is highly coupled with mobilization of PSV reserves, allowing de novo synthesis of various hydrolases in aleurone cells for endosperm degradation. Here we show that in barley (Hordeum vulgare L.) oleosins, the major integral proteins of oleosomes are encoded by four genes (HvOle1 to 4), and the expression of HvOle1 and HvOle3 is strongly up-regulated by abscisic acid (ABA), which shows antagonism to gibberellic acid. In aleurone cells, all HvOLEs were subcellularly targeted to the tonoplast of PSVs. Gain-of-function analyses revealed that HvOLE3 effectively delayed PSV coalescence, whereas HvOLE1 only had a moderate effect, with no notable effect of HvOLE2 and 4. With regard to longevity, HvOLE3 chiefly outperformed other HvOLEs, followed by HvOLE1. Experiments swapping the N- and C-terminal domain between HvOLE3 and other HvOLEs showed that the N-terminal region of HvOLE3 is mainly responsible, with some positive effect by the C-terminal region, for mediating the specific preventive effect of HvOLE3 on PSV coalescence. Three ACGT-core elements and the RY-motif were responsible for ABA induction of HvOle3 promoter activity. Transient expression assays using aleurone protoplasts demonstrated that transcriptional activation of the HvOle3 promoter was mediated by transcription factors HvABI3 and HvABI5, which acted downstream of protein kinase HvPKABA1.
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Affiliation(s)
- Sung-Eun Lee
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - In Sun Yoon
- Gene Engineering Division, National Institute of Agricultural Sciences, Jeonju 565-851, Republic of Korea
| | - Yong-Sic Hwang
- Department of Systems Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
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34
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Luo J, Chen J, Guo W, Yang Z, Lim KJ, Wang Z. Reassessment of Annamocarya sinesis ( Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis. Plants (Basel) 2021; 11:plants11010052. [PMID: 35009055 PMCID: PMC8747223 DOI: 10.3390/plants11010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 05/20/2023]
Abstract
Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species' chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.
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Affiliation(s)
- Jie Luo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Department of Biology, Saint Louis University, St. Louis, MO 63104, USA
| | - Wenlei Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, Hangzhou 311300, China; (J.L.); (J.C.); (W.G.); (Z.Y.)
- Correspondence: (K.-J.L.); (Z.W.)
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35
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Fortelný I, Jůza J. The Effects of Copolymer Compatibilizers on the Phase Structure Evolution in Polymer Blends-A Review. Materials (Basel) 2021; 14:ma14247786. [PMID: 34947377 PMCID: PMC8707745 DOI: 10.3390/ma14247786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
This paper summarizes the results of studies describing the effect of block and graft copolymers on the phase structure formation and evolution in immiscible polymer blends. The main phenomenological rules for prediction of the copolymer compatibilization efficiency are briefly described and compared with selected experimental data. The results of the theories of equilibrium distribution of a copolymer between the blend interface and the bulk phases and its effect on the blend interfacial tension are summarized. The theories of the compatibilizer effect on the droplet breakup in flow are analyzed. The mechanisms of the copolymer effect on the coalescence of droplets in flow are compared and their effect on the droplet size is shown. The problems of reliable description of the effect of a copolymer on the coalescence in quiescent state are presented. Obstacles to derivation of a realistic theory of the copolymer effect on the competition between the droplet breakup and coalescence are discussed. Selected experimental data are compared with the theoretical results.
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Molloy EK, Gatesy J, Springer MS. Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone. Syst Biol 2021; 71:721-740. [PMID: 34677617 DOI: 10.1093/sysbio/syab086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100 000 parsimony-informative RIs. We found that, when given just 1 000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e clades separated by branches > 0.3 CUs) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.
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Affiliation(s)
- Erin K Molloy
- Department of Computer Science, University of Maryland, College Park, College Park, 20742, USA
| | - John Gatesy
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, 92521, USA
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Smith MM, Gilbert JH, Olson ER, Scribner KT, Van Deelen TR, Van Stappen JF, Williams BW, Woodford JE, Pauli JN. A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge. Ecol Appl 2021; 31:e02416. [PMID: 34278627 DOI: 10.1002/eap.2416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated across much of the Great Lakes region by the 1930s and, despite multiple translocations beginning in the 1950s, martens remain of regional conservation concern. Surprisingly, martens were rediscovered in 2014 on the Apostle Islands of Lake Superior after a putative absence of >40 yr. To identify the source of martens to the islands and understand connectivity of the reintroduction network, we collected genetic data on martens from the archipelago and from all regional reintroduction sites. In total, we genotyped 483 individual martens, 43 of which inhabited the Apostle Islands (densities 0.42-1.46 km-2 ). Coalescent analyses supported the contemporary recolonization of the Apostle Islands with progenitors likely originating from Michigan, which were sourced from Ontario. We also identified movements by a first-order relative between the Apostle Islands and the recovery network. We detected some regional gene flow, but in an unexpected direction: individuals moving from the islands to the mainland. Our findings suggest that the Apostle Islands were naturally recolonized by progeny of translocated individuals and now act as a source back to the reintroduction sites on the mainland. We suggest that the Apostle Islands, given its protection from disturbance, complex forest structure, and reduced carnivore competition, will act as a potential refuge for marten along their trailing range boundary and a central node for regional recovery. Our work reveals that translocations, even those occurring along southern range boundaries, can create recovery networks that function like natural metapopulations. Identifying refuges, locations that are resistant to environmental change, within these recovery networks can further improve species recovery, even within novel environments. Future translocation planning should a priori identify potential refuges and sources to improve short-term recovery and long-term persistence.
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Affiliation(s)
- Matthew M Smith
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Jonathan H Gilbert
- Great Lakes Indian Fish and Wildlife Commission, Odanah, Wisconsin, 54861, USA
| | - Erik R Olson
- Department of Natural Resources, Northland College, Ashland, Wisconsin, 54806, USA
| | - Kim T Scribner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Timothy R Van Deelen
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Julie F Van Stappen
- Apostle Islands National Lakeshore, National Park Service, Bayfield, Wisconsin, 54814, USA
| | - Bronwyn W Williams
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27699, USA
| | - James E Woodford
- Bureau of Natural Heritage Conservation, Wisconsin Department of Natural Resources, Rhinelander, Wisconsin, 54501, USA
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, 53706, USA
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Zhang Z, Qiang J, Wang S, Xu M, Gan M, Rao Z, Tian T, Ke S, Zhou Y, Hu Y, Leung CW, Mak CL, Fei L. Visualization of Bubble Nucleation and Growth Confined in 2D Flakes. Small 2021; 17:e2103301. [PMID: 34473395 DOI: 10.1002/smll.202103301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The nucleation and growth of bubbles within a solid matrix is a ubiquitous phenomenon that affects many natural and synthetic processes. However, such a bubbling process is almost "invisible" to common characterization methods because it has an intrinsically multiphased nature and occurs on very short time/length scales. Using in situ transmission electron microscopy to explore the decomposition of a solid precursor that emits gaseous byproducts, the direct observation of a complete nanoscale bubbling process confined in ultrathin 2D flakes is presented here. This result suggests a three-step pathway for bubble formation in the confined environment: void formation via spinodal decomposition, bubble nucleation from the spherization of voids, and bubble growth by coalescence. Furthermore, the systematic kinetics analysis based on COMSOL simulations shows that bubble growth is actually achieved by developing metastable or unstable necks between neighboring bubbles before coalescing into one. This thorough understanding of the bubbling mechanism in a confined geometry has implications for refining modern nucleation theories and controlling bubble-related processes in the fabrication of advanced materials (i.e., topological porous materials).
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Affiliation(s)
- Zhouyang Zhang
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Jun Qiang
- State Key Laboratory of High-Performance Complex Manufacturing, College of Mechanical and Electrical Engineering, Central South University, Changsha, Hunan, 410083, China
| | - Shensong Wang
- Hubei Key Laboratory of Ferro- & Piezoelectric Materials and Devices, School of Microelectronics, Hubei University, Wuhan, Hubei, 430062, China
| | - Ming Xu
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Min Gan
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Zhenggang Rao
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Tingfang Tian
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Shanming Ke
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Yangbo Zhou
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Yongming Hu
- Hubei Key Laboratory of Ferro- & Piezoelectric Materials and Devices, School of Microelectronics, Hubei University, Wuhan, Hubei, 430062, China
| | - Chi Wah Leung
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Chee Leung Mak
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Linfeng Fei
- School of Materials Science and Engineering, Jiangxi Engineering Laboratory for Advanced Functional Thin Films, Jiangxi Key Laboratory for Two-Dimensional Materials and Jiangxi Key Laboratory for Multiscale Interdisciplinary Study, Nanchang University, Nanchang, Jiangxi, 330031, China
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Niinivaara E, Ouzas A, Fraschini C, Berry RM, Dubé MA, Cranston ED. How latex film formation and adhesion at the nanoscale correlate to performance of pressure sensitive adhesives with cellulose nanocrystals. Philos Trans A Math Phys Eng Sci 2021; 379:20200330. [PMID: 34334024 DOI: 10.1098/rsta.2020.0330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/11/2021] [Indexed: 06/13/2023]
Abstract
Emulsion polymerized latex-based pressure-sensitive adhesives (PSAs) are more environmentally benign because they are synthesized in water but often underperform compared to their solution polymerized counterparts. Studies have shown a simultaneous improvement in the tack, and peel and shear strength of various acrylic PSAs upon the addition of cellulose nanocrystals (CNCs). This work uses atomic force microscopy (AFM) to examine the role of CNCs in (i) the coalescence of hydrophobic 2-ethyl hexyl acrylate/n-butyl acrylate/methyl methacrylate (EHA/BA/MMA) latex films and (ii) as adhesion modifiers over multiple length scales. Thin films with varying solids content and CNC loading were prepared by spin coating. AFM revealed that CNCs lowered the solids content threshold for latex particle coalescence during film formation. This improved the cohesive strength of the films, which was directly reflected in the increased shear strength of the EHA/BA/MMA PSAs with increasing CNC loading. Colloidal probe AFM indicated that the nano-adhesion of thicker continuous latex films increased with CNC loading when measured over small contact areas where the effect of surface roughness was negligible. Conversely, the beneficial effects of the CNCs on macroscopic PSA tack and peel strength were outweighed by the effects of increased surface roughness with increasing CNC loading over larger surface areas. This highlights that CNCs can improve both cohesive and adhesive PSA properties; however, the effects are most pronounced when the CNCs interact favourably with the latex polymer and are uniformly dispersed throughout the adhesive film. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.
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Affiliation(s)
- Elina Niinivaara
- Chemical Engineering Department, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Vuorimiehentie 1, 0076 Aalto, Espoo, Finland
| | - Alexandra Ouzas
- Department of Chemical and Biological Engineering, Centre for Catalysis Research and Innovation, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Carole Fraschini
- FPInnovations, 570 Saint-Jean Boulevard, Pointe Claire, Quebec, Canada H9R 3J9
| | - Richard M Berry
- CelluForce Inc., 570, Boulevard Saint-Jean, Pointe-Claire, Quebec, H9R 3J9
| | - Marc A Dubé
- Department of Chemical and Biological Engineering, Centre for Catalysis Research and Innovation, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Emily D Cranston
- Chemical Engineering Department, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada V6T 1Z4
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, British Columbia, Canada V6T 1Z3
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Wu Y, Dong Q, He J. The Effect of Chemical Corrosion on Mechanics and Failure Behaviour of Limestone Containing a Single Kinked Fissure. Sensors (Basel) 2021; 21:5641. [PMID: 34451082 DOI: 10.3390/s21165641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
This study concerns the influence of chemical corrosion and geometric parameters on the macroscopic damage characteristics of brittle limestone containing a kinked fissure under uniaxial compression. The specimens are prepared in chemical solutions with different NaCl concentrations and pH values. The acoustic emission (AE) technique is adopted to detect the inner distortion of the failure behaviour. The physical process of the crack coalescence of kinked fissures is synchronously captured by a high-speed camera. Seven failure patterns are identified based on the final failure mode and the failure process. Furthermore, the stress intensity factor of kinked cracks under chemical corrosion is obtained by a theoretical analysis. Chemical erosion with an acidic solution has a relatively strong effect on the compressive strength of the tested specimen, while the initial crack angle is not affected by short-term chemical corrosion.
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Lesturgie P, Planes S, Mona S. Coalescence times, life history traits and conservation concerns: An example from four coastal shark species from the Indo-Pacific. Mol Ecol Resour 2021; 22:554-566. [PMID: 34407294 DOI: 10.1111/1755-0998.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographical ranges and less mobile ones organized in metapopulations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne ) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (metapopulation) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.
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Affiliation(s)
- Pierre Lesturgie
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB (UMR 7205), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia.,EPHE, PSL Research University, Paris, France
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Bierwisch C. Consistent Thermo-Capillarity and Thermal Boundary Conditions for Single-Phase Smoothed Particle Hydrodynamics. Materials (Basel) 2021; 14:4530. [PMID: 34443055 DOI: 10.3390/ma14164530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022]
Abstract
A model for capillary phenomena including temperature-dependency and thermal boundary conditions is presented in the numerical framework of smoothed particle hydrodynamics (SPH). The model requires only a single fluid phase and is therefore computationally more efficient than surface tension schemes which need an explicit fluid-fluid or fluid-gas interface. The model makes use of a surface identification mechanism based on the SPH renormalization tensor. All relevant properties of the continuum surface force (CSF) based approach, i.e., the delta function, normal vector and curvature, are calculated in a consistent manner. The model is parametrized by physical material properties and is successfully validated by means of a large set of analytical test cases. The applicability of the proposed model to more complex scenarios is demonstrated.
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Thomas SK, Liu X, Du Z, Dong Y, Cummings A, Pokorny L, Xiang Q(J, Leebens‐Mack JH. Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set. Am J Bot 2021; 108:1112-1121. [PMID: 34263456 PMCID: PMC8361741 DOI: 10.1002/ajb2.1696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/12/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales. METHODS Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae. RESULTS We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL-III, a method statistically consistent with the multispecies coalescent model. CONCLUSIONS The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae-Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.
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Affiliation(s)
- Shawn K. Thomas
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Division of Biological SciencesUniversity of MissouriColumbiaMO65203USA
| | - Xiang Liu
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- SyngentaResearch Triangle ParkNC27709USA
| | - Zhi‐Yuan Du
- Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanHubei430074China
| | - Yibo Dong
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- Global Health Infectious Disease ResearchCollege of Public HealthUniversity of South FloridaTampaFL33612USA
| | - Amanda Cummings
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondLondonTW9 3AEUK
- Computational/Systems Biology and Genomics ProgramCentre for Plant Biotechnology and GenomicsUPM‐INIA‐CSICPozuelo de Alarcón (Madrid)28223Spain
| | - Qui‐Yun (Jenny) Xiang
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
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Ottenlips MV, Mansfield DH, Buerki S, Feist MAE, Downie SR, Dodsworth S, Forest F, Plunkett GM, Smith JF. Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex. Am J Bot 2021; 108:1217-1233. [PMID: 34105148 PMCID: PMC8362113 DOI: 10.1002/ajb2.1676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/26/2021] [Indexed: 05/29/2023]
Abstract
PREMISE Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.
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Affiliation(s)
| | | | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
| | | | - Stephen R. Downie
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Steven Dodsworth
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
- School of Life SciencesUniversity of BedfordshireLutonLU1 3JUUK
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
| | - Gregory M. Plunkett
- Cullman Program for Molecular SystematicsNew York Botanical Garden2900 Southern BoulevardBronxNY10458USA
| | - James F. Smith
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. Am J Bot 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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46
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Paszek J, Markin A, Górecki P, Eulenstein O. Taming the Duplication-Loss- Coalescence Model with Integer Linear Programming. J Comput Biol 2021; 28:758-773. [PMID: 34125600 DOI: 10.1089/cmb.2021.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The duplication-loss-coalescence (DLC) parsimony model is invaluable for analyzing the complex scenarios of concurrent duplication loss and deep coalescence events in the evolution of gene families. However, inferring such scenarios for already moderately sized families is prohibitive owing to the computational complexity involved. To overcome this stringent limitation, we make the first step by describing a flexible integer linear programming (ILP) formulation for inferring DLC evolutionary scenarios. Then, to make the DLC model more scalable, we introduce four sensibly constrained versions of the model and describe modified versions of our ILP formulation reflecting these constraints. Our simulation studies showcase that our constrained ILP formulations compute evolutionary scenarios that are substantially larger than scenarios computable under our original ILP formulation and the original dynamic programming algorithm by Wu et al. Furthermore, scenarios computed under our constrained DLC models are remarkably accurate compared with corresponding scenarios under the original DLC model, which we also confirm in an empirical study with thousands of gene families.
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Affiliation(s)
- Jarosław Paszek
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Alexey Markin
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
| | - Paweł Górecki
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
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47
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Shen CZ, Zhang CJ, Chen J, Guo YP. Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae). Front Plant Sci 2021; 12:648026. [PMID: 34122473 PMCID: PMC8187803 DOI: 10.3389/fpls.2021.648026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/20/2021] [Indexed: 05/12/2023]
Abstract
Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.
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Affiliation(s)
- Chu-Ze Shen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Chu-Jie Zhang
- School of Life Sciences, Peking University, Beijing, China
| | - Jie Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Yan-Ping Guo
- School of Life Sciences, Peking University, Beijing, China
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48
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Takamura K, Ueno R, Kondo NI, Ohbayashi K. Pond chironomid communities revealed by molecular species delimitation reflect eutrophication. Ecol Evol 2021; 11:4193-4204. [PMID: 33976803 PMCID: PMC8093717 DOI: 10.1002/ece3.7315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 11/26/2022] Open
Abstract
Farm ponds, a valued habitat for freshwater organisms, are being negatively affected by the recent changes in the environment as well as anthropological activities. In these ponds, biodiversity researchers have tended to focus on species that prefer natural habitats and/or can be identified based on morphological characters. In contrast, this study focused on the insect family Chironomidae, which is widely distributed from clear to polluted waters of ponds, but is hard to identify morphologically as an aquatic larva. We adopted DNA barcoding and molecular species delimitation to identify every single specimen of quantitative collections. From bottom sediments of 17 ponds in summer in the Banshu Plain of Japan, a total of 62 species were delimited based on the DNA sequences of the mitochondrial COI region. Chironomid communities from these ponds were classified into four groups in a two-dimensional ordination of multivariate analysis (NMDS). One of the dimensions was well correlated with the gradient of eutrophication, while another dimension was not clearly assigned to any general feature of the environmental gradient, but rice cultivation could possibly be involved.
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Affiliation(s)
- Kenzi Takamura
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Ryuhei Ueno
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Natsuko Ito Kondo
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Kako Ohbayashi
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
- Graduate School of Arts and SciencesThe University of TokyoKomabaJapan
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49
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Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Curr Biol 2021; 31:1653-1665.e5. [PMID: 33607033 PMCID: PMC8347878 DOI: 10.1016/j.cub.2021.01.074] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 12/22/2022]
Abstract
Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Department of Biological Sciences, University of Toronto Scarborough and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, 3584 CT, Utrecht 85167, the Netherlands
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xing-Xing Shen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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50
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Yuan B, Cademartiri L. Growth of Colloidal Nanocrystals by Liquid-Like Coalescence*. Angew Chem Int Ed Engl 2021; 60:6667-6672. [PMID: 33326683 DOI: 10.1002/anie.202014275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/30/2020] [Indexed: 11/10/2022]
Abstract
We here describe, model, and predict the growth kinetics of amine-capped PbS colloidal nanoparticles in the absence of supersaturation. The particles grow by coalescence rather than by Ostwald ripening. A comparison of different models indicates that the effective activation energy of coalescence (67.65 kJ mol-1 ) is associated with two terms: a term proportional to the contact area between the ligand shells of two colliding particles, and a constant term. Our Brownian dynamics simulations show (i) how the remarkably low activation energy (or large rate constants) are most likely due to the large difference in size between the particles and their mean free path of diffusion, and (ii) how the low polydispersity is the likely result of the suppression of collision rates between rare populations due to crowding. The model successfully predicts the growth kinetics of nanoparticles, therefore enabling the precise control of the average particle size without the need of supersaturation.
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Affiliation(s)
- Bin Yuan
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, 2220 Hoover Hall, Ames, IA, 50011, USA.,Department of Chemical & Biological Engineering, Iowa State University of Science and Technology, Sweeney Hall, Ames, IA, 50011, USA.,Current address: Mechanical Engineering Department, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Ludovico Cademartiri
- Department of Materials Science & Engineering, Iowa State University of Science and Technology, 2220 Hoover Hall, Ames, IA, 50011, USA.,Department of Chemical & Biological Engineering, Iowa State University of Science and Technology, Sweeney Hall, Ames, IA, 50011, USA.,Ames Laboratory, U.S. Department of Energy, Ames, IA, 50011, USA.,Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
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